Synthesis of Anthraquinone Derivatives and their Conjugates with 2\u27-Deoxynucleosides as New Probes for Electron Transfer Studies in DNA

Anthraquinone (AQ) has been used in electron transfer studies in DNA. The focus of this dissertation is the synthesis of conjugates between AQ derivatives and 2’-deoxyadenosine (dA), which can be used to induce adenine oxidation in DNA. Different AQ derivatives were attached to dA via ethynyl or ethanyl linkers. If incorporated into DNA, these short linkers should enable regiocontrol for electron transfer from adenine within the DNA duplex structure. The challenge in working with anthraquinone-2’-deoxynucleosides conjugates is that they and their intermediates are insoluble in water and only sparingly soluble in most organic solvents. A strategy used to overcome this problem was the use of either tert-butyldiphenylsilyl (TBDPS) or 4’,4-dimethoxytrityl (DMTr) 5’-protected deoxynucleosides as starting materials. A water-soluble, ethynyl-linked AQ-dA conjugate with a 3’-benzyl hydrogen phosphate was synthesized using DMTr protection. The DMTr group was not stable to the hydrogenation required to make the ethanyl-linked AQ-dA conjugate with 3’-benzyl hydrogen phosphate. Hence the latter was synthesized starting with the TBDPS protecting group. Both of these syntheses were based on the Pd coupling between ethynylanthraquinone and 8-bromodeoxyadenosine derivatives. New conjugates between AQ and A, in which the AQ moieties have been modified with formyl, trifluoroacetyl and methyl ester groups as electron withdrawing substituents were also synthesized. The synthesis of these AQ-dA conjugates was based on Pd coupling between bromoanthraquinone and 8-ethynyldeoxyadenosine derivatives. This route avoided the use of ethynylanthraquinone derivatives that had extremely low solubility and photoinstability. Other anthraquinones with electron withdrawing groups (which should provide enhanced driving force to enable respective AQ derivative to oxidize adenine) were synthesized as models. Cyclic voltammetry showed that the conjugate with the two ester groups and ethynyl linker was the most easily reduced of the derivatives synthesized. Conjugates between AQ and dU were also synthesized. Those conjugates can potentially be used to oxidize guanine or adenine or they can be used as a deep trap for an electron in reduced DNA

Lithium Hexamethyldisilazane Transformation of Transiently Protected 4‑Aza/Benzimidazole Nitriles to Amidines and their Dimethyl Sulfoxide Mediated Imidazole Ring Formation

Trimethylsilyl-transient protection successfully allowed the use of lithium hexamethyldisilazane to prepare benzimidazole (BI) and 4-azabenzimidazole (azaBI) amidines from nitriles in 58–88% yields. This strategy offers a much better choice to prepare BI/azaBI amidines than the lengthy, low-yielding Pinner reaction. Synthesis of aza/benzimidazole rings from aromatic diamines and aldehydes was affected in dimethyl sulfoxide in 10–15 min, while known procedures require long time and purification. These methods are important for the BI/azaBI-based drug industry and for developing specific DNA binders for expanded therapeutic applications

Fluorescence-Based Binding Characterization of Small Molecule Ligands Targeting CUG RNA Repeats

Pathogenic CUG and CCUG RNA repeats have been associated with myotonic dystrophy type 1 and 2 (DM1 and DM2), respectively. Identifying small molecules that can bind these RNA repeats is of great significance to develop potential therapeutics to treat these neurodegenerative diseases. Some studies have shown that aminoglycosides and their derivatives could work as potential lead compounds targeting these RNA repeats. In this work, sisomicin, previously known to bind HIV-1 TAR, is investigated as a possible ligand for CUG RNA repeats. We designed a novel fluorescence-labeled RNA sequence of r(CUG)10 to mimic cellular RNA repeats and improve the detecting sensitivity. The interaction of sisomicin with CUG RNA repeats is characterized by the change of fluorescent signal, which is initially minimized by covalently incorporating the fluorescein into the RNA bases and later increased upon ligand binding. The results show that sisomicin can bind and stabilize the folded RNA structure. We demonstrate that this new fluorescence-based binding characterization assay is consistent with the classic UV Tm technique, indicating its feasibility for high-throughput screening of ligand-RNA binding interactions and wide applications to measure the thermodynamic parameters in addition to binding constants and kinetics when probing such interactions

Design and Synthesis of Newly Synthesized Acrylamide Derivatives as Potential Chemotherapeutic Agents against MCF-7 Breast Cancer Cell Line Lodged on PEGylated Bilosomal Nano-Vesicles for Improving Cytotoxic Activity

Cancer is a multifaceted disease. With the development of multi drug resistance, the need for the arousal of novel targets in order to avoid these drawbacks increased. A new series of acrylamide derivatives was synthesized from starting material 4-(furan-2-ylmethylene)-2-(3,4,5-trimethoxyphenyl)oxazol-5(4H)–one (1), and they are evaluated for their inhibitory activity against β-tubulin polymerization. The target molecules 2–5 d were screened for their cytotoxic activity against breast cancer MCF-7 cell line. The results of cytotoxicity screening revealed that compounds 4e and 5d showed good cytotoxic profile against MCF-7 cells. Compounds 4e produced significant reduction in cellular tubulin with excellent β-tubulin polymerization inhibition activity. In addition, compound 4e exhibited cytotoxic activity against MCF-7 cells by cell cycle arrest at pre-G1 and G2/M phases, as shown by DNA flow cytometry assay. Aiming to enhance the limited aqueous solubility and, hence, poor oral bioavailability of the prepared lead acrylamide molecule, 4e-charged PEGylated bilosomes were successfully fabricated via thin film hydration techniques as an attempt to improve these pitfalls. 23 full factorial designs were manipulated to examine the influence of formulation variables: types of bile salt including either sodium deoxy cholate (SDC) or sodium tauro cholate (STC), amount of bile salt (15 mg or 30 mg) and amount of DSPE–mPEG-2000 amount (25 mg or 50 mg) on the characteristics of the nanosystem. The F7 formula of entrapment efficiency (E.E% = 100 ± 5.6%), particle size (PS = 280.3 ± 15.4 nm) and zeta potential (ZP = −22.5 ± 3.4 mv) was picked as an optimum formula with a desirability value of 0.868. Moreover, prominent enhancement was observed at the compound’s cytotoxic activity (IC50 = 0.75 ± 0.03 µM) instead of (IC50 = 2.11 ± 0.19 µM) for the unformulated 4e after being included in the nano-PEGylated bilosomal system